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- PDB-6z2h: Citryl-CoA lyase module of human ATP citrate lyase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6z2h
TitleCitryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.
ComponentsATP-citrate synthase
KeywordsLYASE / acetyl-CoA production / metabolism / atp citrate lyase / lipogenesis
Function / homology
Function and homology information


ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol
Similarity search - Function
ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase ...ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / OXALOACETATE ION / (3S)-citryl-Coenzyme A / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVerschueren, K.H.G. / Verstraete, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0619N Belgium
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2021
Title: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.
Authors: Verstraete, K. / Verschueren, K.H.G. / Dansercoer, A. / Savvides, S.N.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Sep 22, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_related / software
Item: _pdbx_database_related.db_name / _software.classification
Revision 1.5Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,73811
Polymers120,0324
Non-polymers4,7067
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, In solution oligomeric state confirmed via SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26640 Å2
ΔGint-186 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.436, 114.271, 144.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 30008.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Prior to crystallisation, the N-terminal His-tag (MGSSHHHHHHSSGLVPR) was removed by thrombin cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET15b / Details (production host): N-terminal cleavable His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53396, ATP citrate synthase
#2: Chemical ChemComp-Q5B / (3S)-citryl-Coenzyme A / (2~{S})-2-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid


Mass: 941.642 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C27H42N7O22P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium actetate pH 7.0 20 % PEG3350 65 mM oxaloacetate 7 mM acetyl-CoA

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2018
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 105289 / % possible obs: 99.7 % / Redundancy: 15.06 % / Biso Wilson estimate: 20.86 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.15 / Net I/σ(I): 15.02
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 16581 / CC1/2: 0.782 / Rrim(I) all: 1.208 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hxl

6hxl


Resolution: 1.8→44.28 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1923 5260 5 %
Rwork0.1578 100011 -
obs0.1596 105271 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8026 0 300 623 8949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01048745
X-RAY DIFFRACTIONf_angle_d1.108611891
X-RAY DIFFRACTIONf_chiral_restr0.05681310
X-RAY DIFFRACTIONf_plane_restr0.00691554
X-RAY DIFFRACTIONf_dihedral_angle_d12.10381369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.3271570.27083042X-RAY DIFFRACTION92.62
1.82-1.840.31861740.24333321X-RAY DIFFRACTION99.97
1.84-1.860.28641740.23273277X-RAY DIFFRACTION100
1.86-1.890.25071720.22133293X-RAY DIFFRACTION99.97
1.89-1.910.28311760.22063327X-RAY DIFFRACTION100
1.91-1.940.26521730.22383298X-RAY DIFFRACTION100
1.94-1.960.24981750.20733315X-RAY DIFFRACTION100
1.96-1.990.26641740.2073297X-RAY DIFFRACTION100
1.99-2.030.2651750.20623329X-RAY DIFFRACTION100
2.03-2.060.22041720.1843285X-RAY DIFFRACTION99.97
2.06-2.090.20541760.16643318X-RAY DIFFRACTION100
2.09-2.130.19371750.15513331X-RAY DIFFRACTION100
2.13-2.170.19591740.16073296X-RAY DIFFRACTION100
2.17-2.220.2291750.15183335X-RAY DIFFRACTION100
2.22-2.270.20431740.15743312X-RAY DIFFRACTION100
2.27-2.320.19511750.15253332X-RAY DIFFRACTION99.97
2.32-2.380.20021750.14773325X-RAY DIFFRACTION100
2.38-2.440.1841770.13943344X-RAY DIFFRACTION100
2.44-2.510.1781740.13913325X-RAY DIFFRACTION100
2.51-2.590.18291740.14163304X-RAY DIFFRACTION100
2.59-2.690.1951770.14053342X-RAY DIFFRACTION100
2.69-2.790.16831770.14813372X-RAY DIFFRACTION100
2.79-2.920.21221760.15093342X-RAY DIFFRACTION100
2.92-3.070.191760.15643361X-RAY DIFFRACTION99.97
3.07-3.270.19211780.16633381X-RAY DIFFRACTION100
3.27-3.520.1911770.16213347X-RAY DIFFRACTION100
3.52-3.870.17511790.14343405X-RAY DIFFRACTION100
3.87-4.430.13941790.12433412X-RAY DIFFRACTION100
4.43-5.580.14451820.13033449X-RAY DIFFRACTION100
5.59-44.280.17041880.16163594X-RAY DIFFRACTION99.74

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